No longer can the genetic and epigenetic causes of cancer and the resulting changes in gene expression be analyzed separately, with little regard for their interdependency.
In this spirit, Jeremy Squire and coworkers at the Hospital for Sick Children, the Ontario Cancer Institute, and Queen’s University (all in Canada) conducted the first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression.
The researchers used Affymetrix Promoter Tiling Arrays for DNA methylation profiling, the Agilent array-CGH platform for the detection of genomic imbalance, and the Affymetrix Gene 1.0 platform for gene expression analysis to identify changes in two osteosarcoma cell lines compared with normal osteoblasts. Data from these analyses were integrated to reveal genes that showed different layers of epigenetic, genetic, and gene expression changes, for example, hypomethylation, genomic gain, and overexpression. In many cases, genetic and epigenetic mechanisms worked in concert to deregulate gene expression networks in osteosarcoma cells. PLoS ONE, August 2008